Search results for: nuclear power

Authors: Wee Leong Son, Hasmayadi Abdul Majid, Rohana Musa

Abstract:

This paper study the segmented split capacitor Digital-to-Analog Converter (DAC) implemented in a differentialtype 12-bit Successive Approximation Analog-to-Digital Converter (SA-ADC). The series capacitance split array method employed as it reduced the total area of the capacitors required for high resolution DACs. A 12-bit regular binary array structure requires 2049 unit capacitors (Cs) while the split array needs 127 unit Cs. These results in the reduction of the total capacitance and power consumption of the series split array architectures as to regular binary-weighted structures. The paper will show the 12-bit DAC series split capacitor with 4-bit thermometer coded DAC architectures as well as the simulation and measured results.

Keywords: Successive Approximation Register Analog-to- Digital Converter, SAR ADC, Low voltage ADC.

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Authors: Jin-Tsann Yeh, Chyong-Ling Lin

Abstract:

Healthcare providers sometimes use the power of humor as a treatment and therapy for buffering mental health or easing mental disorders because humor can provide relief from distress and conflict. Humor is also very suitable for advertising because of similar benefits. This study carefully examines humor's widespread use in advertising and identifies relationships among humor mechanisms, female depictions, and product types. The purpose is to conceptualize how humor theories can be used not only to successfully define a product as fitting within one of four color categories of the product color matrix, but also to identify compelling contemporary female depictions through humor in ads. The results can offer an idealization for marketing managers and consumers to help them understand how female role depictions can be effectively used with humor in ads. The four propositions developed herein are derived from related literature, through the identification of marketing strategy formulations that achieve product memory enhancement by adopting humor mechanisms properly matched with female role depictions.

Keywords: Humor mechanisms, Female role depiction, Product types.

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Authors: M. R. Aghaebrahimi, H. Khorashadi Zadeh

Abstract:

This paper presents a new approach for busbar protection with stable operation of current transformer during saturation, using fuzzy neuro and symmetrical components theory. This technique uses symmetrical components of current signals to learn the hidden relationship existing in the input patterns. Simulation studies are preformed and the influence of changing system parameters such as inception fault and source impedance is studied. Details of the design procedure and the results of performance studies with the proposed relay are given in the paper. An analysis of the performance of the proposed technique during ct saturation conditions is presented. The performance of the technique was investigated for a variety of operating conditions and for several busbar configurations. Data generated by EMTDC simulations of model power systems were used in the investigations. The results indicate that the proposed technique is stable during ct saturation conditions.

Keywords: Busbar protection, fuzzy neuro, Ct saturation.

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Authors: A.R.Tahmasebi Birgani, M.Hosseinjani Zamenjani, M.R.Isvandzibaei

Abstract:

Study is on the vibration of thin cylindrical shells made of a functionally gradient material (FGM) composed of stainless steel and nickel is presented. The effects of the FGM configuration are studied by studying the frequencies of FG cylindrical shells. In this case FG cylindrical shell has Nickel on its inner surface and stainless steel on its outer surface. The study is carried out based on third order shear deformation shell theory. The objective is to study the natural frequencies, the influence of constituent volume fractions and the effects of configurations of the constituent materials on the frequencies. The properties are graded in the thickness direction according to the volume fraction power-law distribution. Results are presented on the frequency characteristics, the influence of the constituent various volume fractions on the frequencies.

Keywords: Nickel, Stainless Steel, Cylindrical shell.

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Authors: Julian David Hunt, Andreas Nascimento

Abstract:

Green hydrogen is the most environmental, renewable alternative to produce hydrogen. However, an important challenge to make hydrogen a competitive energy carrier is a constant supply of renewable energy, such as solar, wind and hydropower. Given that the electricity generation potential of these sources vary seasonally and interannually, this paper proposes installing an electrolysis hydrogen production plant in a ship and move the ship to the locations where electricity is cheap, or where the seasonal potential for renewable generation is high. An example of electrolysis ship application is to produce green hydrogen with hydropower from the North region of Brazil and then sail to the Northeast region of Brazil and generate hydrogen using excess electricity from offshore wind power. The electrolysis ship concept is interesting because it has the flexibility to produce green hydrogen using the cheapest renewable electricity available in the market.

Keywords: Green hydrogen, electrolysis ship, renewable energies, seasonal variations.

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Authors: S. Chokri

Abstract:

Load modeling is one of the central functions in power systems operations. Electricity cannot be stored, which means that for electric utility, the estimate of the future demand is necessary in managing the production and purchasing in an economically reasonable way. A majority of the recently reported approaches are based on neural network. The attraction of the methods lies in the assumption that neural networks are able to learn properties of the load. However, the development of the methods is not finished, and the lack of comparative results on different model variations is a problem. This paper presents a new approach in order to predict the Tunisia daily peak load. The proposed method employs a computational intelligence scheme based on the Fuzzy neural network (FNN) and support vector regression (SVR). Experimental results obtained indicate that our proposed FNN-SVR technique gives significantly good prediction accuracy compared to some classical techniques.

Keywords: Neural network, Load Forecasting, Fuzzy inference, Machine learning, Fuzzy modeling and rule extraction, Support Vector Regression.

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Authors: Mona Almansoori, Ahmed Mustafa, Ahmad Elshamy

Abstract:

Wireless sensor network was formed by a combination of nodes, systematically it transmitting the data to their base stations, this transmission data can be easily compromised if the limited processing power and the data consistency from these nodes are kept in mind; there is always a discussion to address the secure data transfer or transmission in actual time. This will present a mechanism to securely transmit the data over a chain of sensor nodes without compromising the throughput of the network by utilizing available battery resources available in the sensor node. Our methodology takes many different advantages of Z-MAC protocol for its efficiency, and it provides a unique key by sharing the mechanism using neighbor node MAC address. We present a light weighted data integrity layer which is embedded in the Z-MAC protocol to prove that our protocol performs well than Z-MAC when we introduce the different attack scenarios.

Keywords: Hybrid MAC protocol, data integrity, lightweight encryption, Neighbor based key sharing, Sensor node data processing, Z-MAC.

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Authors: Michiko Miyamoto

Abstract:

This paper empirically investigates whether information technology (IT) strategies, business strategies, and divisions are aligned to meet overall business goals for Korean Small and medium-sized enterprises (SMEs), based on structure based Strategic Alignment Model, and make comparison with those of Japanese SMEs. Using 2,869 valid responses of Korean Human Capital Corporate Panel survey, a result of this study suggests that Korean human resources (HR) departments have a major influence over IT strategy, which is the same as Japanese SMEs, even though their management styles are quite different. As for IT strategy, it is not related to other departments at all for Korean SMEs. The Korean management seems to possess a great power over each division, such as Sales/Service, Research and Development/Technical Experts, HR, and Production.

Keywords: IT-business alignment, structured based strategic alignment model, structural equation model, human resources department.

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Authors: M.R.Alinaghizadehand, M.R.Isvandzibaei

Abstract:

Study of the vibration cylindrical shells made of a functionally gradient material (FGM) composed of stainless steel and nickel is important. Material properties are graded in the thickness direction of the shell according to volume fraction power law distribution. The objective is to study the natural frequencies, the influence of constituent volume fractions and the effects of boundary conditions on the natural frequencies of the FG cylindrical shell. The study is carried out using third order shear deformation shell theory. The governing equations of motion of FG cylindrical shells are derived based on shear deformation theory. Results are presented on the frequency characteristics, influence of constituent volume fractions and the effects of clampedclamped boundary conditions.

Keywords: Vibration, FGM, Cylindrical shell, Hamilton's principle.

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Authors: M. Nayeripour, T. Niknam

Abstract:

Nonlinear and unbalance loads in three phase networks create harmonics and losses. Active and passive filters are used for elimination or reduction of these effects. Passive filters have some limitations. For example, they are designed only for a specific frequency and they may cause to resonance in the network at the point of common coupling. The other drawback of a passive filter is that the sizes of required elements are normally large. The active filter can improve some of limitations of passive filter for example; they can eliminate more than one harmonic and don't cause resonance in the network. In this paper inverter analysis have been done simultaneously in three phase and the RL impedance of the line have been considered. A sliding mode control based on energy feedback of capacitors is employed in the design with this method, the dynamic speed of the filter is improved effectively and harmonics and load unbalance is compensating quickly.

Keywords: Shunt active filter, harmonic, inverter, sliding mode control, energy feedback.

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Authors: V. Masilamani, D.K. Sheena Christy, D.G. Thomas

Abstract:

Image synthesis is an important area in image processing. To synthesize images various systems are proposed in the literature. In this paper, we propose a bio-inspired system to synthesize image and to study the generating power of the system, we define the class of languages generated by our system. We call image as array in this paper. We use a primitive called iso-array to synthesize image/array. The operation is double splicing on iso-arrays. The double splicing operation is used in DNA computing and we use this to synthesize image. A comparison of the family of languages generated by the proposed self restricted double splicing systems on iso-arrays with the existing family of local iso-picture languages is made. Certain closure properties such as union, concatenation and rotation are studied for the family of languages generated by the proposed model.

Keywords: DNA computing, splicing system, iso-picture languages, iso-array double splicing system, iso-array self splicing.

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Authors: N. A. Muhamad, S.A.M. Ali

Abstract:

Condition monitoring of electrical power equipment has attracted considerable attention for many years. The aim of this paper is to use Labview with Fuzzy Logic controller to build a simulation system to diagnose transformer faults and monitor its condition. The front panel of the system was designed using LabVIEW to enable computer to act as customer-designed instrument. The dissolved gas-in-oil analysis (DGA) method was used as technique for oil type transformer diagnosis; meanwhile terminal voltages and currents analysis method was used for dry type transformer. Fuzzy Logic was used as expert system that assesses all information keyed in at the front panel to diagnose and predict the condition of the transformer. The outcome of the Fuzzy Logic interpretation will be displayed at front panel of LabVIEW to show the user the conditions of the transformer at any time.

Keywords: LabVIEW, Fuzzy Logic, condition monitoring, oiltransformer, dry transformer, DGA, terminal values.

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Authors: Huiming Peng, Jianguo Wen, Hongwei Li, Jeff Chang, Xiaobo Zhou

Abstract:

NFκB activation plays a crucial role in anti-apoptotic responses in response to the apoptotic signaling during tumor necrosis factor (TNFa) stimulation in Multiple Myeloma (MM). Although several drugs have been found effective for the treatment of MM by mainly inhibiting NFκB pathway, there are no any quantitative or qualitative results of comparison assessment on inhibition effect between different single drugs or drug combinations. Computational modeling is becoming increasingly indispensable for applied biological research mainly because it can provide strong quantitative predicting power. In this study, a novel computational pathway modeling approach is employed to comparably assess the inhibition effects of specific single drugs and drug combinations on the NFκB pathway in MM, especially the prediction of synergistic drug combinations.

Keywords: Computational modeling, drug combination, inhibition effect, multiple myeloma, NFkB pathway.

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Authors: Tanja Radu, Cormac Fay, King Tong Lau, Rhys Waite, Dermot Diamond

Abstract:

The development of wearable sensing technologies is a great challenge which is being addressed by the Proetex FP6 project (www.proetex.org). Its main aim is the development of wearable sensors to improve the safety and efficiency of emergency personnel. This will be achieved by continuous, real-time monitoring of vital signs, posture, activity, and external hazards surrounding emergency workers. We report here the development of carbon dioxide (CO2) sensing boot by incorporating commercially available CO2 sensor with a wireless platform into the boot assembly. Carefully selected commercially available sensors have been tested. Some of the key characteristics of the selected sensors are high selectivity and sensitivity, robustness and the power demand. This paper discusses some of the results of CO2 sensor tests and sensor integration with wireless data transmission

Keywords: Proetex, gas sensing, wireless, wearable sensors, carbon dioxide

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Authors: Sungjin Lee, Donghyun Choi, Choonsik Park, Seungjoo Kim

Abstract:

A SCADA (Supervisory Control And Data Acquisition) system is an industrial control and monitoring system for national infrastructures. The SCADA systems were used in a closed environment without considering about security functionality in the past. As communication technology develops, they try to connect the SCADA systems to an open network. Therefore, the security of the SCADA systems has been an issue. The study of key management for SCADA system also has been performed. However, existing key management schemes for SCADA system such as SKE(Key establishment for SCADA systems) and SKMA(Key management scheme for SCADA systems) cannot support broadcasting communication. To solve this problem, an Advanced Key Management Architecture for Secure SCADA Communication has been proposed by Choi et al.. Choi et al.-s scheme also has a problem that it requires lots of computational cost for multicasting communication. In this paper, we propose an enhanced scheme which improving computational cost for multicasting communication with considering the number of keys to be stored in a low power communication device (RTU).

Keywords: SCADA system, SCADA communication, Key management, Distributed networks.

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Authors: Morteza Fathipour, Samira Omidbakhsh, Kimia Khodayari

Abstract:

RF performance of SOI CMOS device has attracted significant amount of interest recently. In order to improve RF parameters, Strained Si/Relaxed Si0.8Ge0.2 investigated as a replacement for Si technology .Enhancement of carrier mobility associated with strain engineering makes Strained Si a promising candidate for improving RF performance of CMOS technology. From the simulation, the cut-off frequency is estimated to be 224 GHZ, whereas in SOI at similar bias is about 188 GHZ. Therefore, Strained Si exhibits 19% improvement in cut-off frequency over similar Si counterpart. In this paper, Ion/Ioff ratio is studied as one of the key parameters in logic and digital application. Strained Si/SiGe demonstrates better Ion/Ioff characteristic than SOI, in similar channel length of 100 nm.Another important key analog figures of merit such as Early Voltage (VEA) ,transconductance vs drain current (gm /Ids) are studied. They introduce the efficiency of the devices to convert dc power into ac frequency.

Keywords: cut-off frequency, RF application, Silicon oninsulator, Strained Si/SiGe on insulator.

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Authors: G.H. Farrahi, S.A. Faghidian, D.J. Smith

Abstract:

A thin layer on the component surface can be found with high tensile residual stresses, due to turning operations, which can dangerously affect the fatigue performance of the component. In this paper an analytical approach is presented to reconstruct the residual stress field from a limited incomplete set of measurements. Airy stress function is used as the primary unknown to directly solve the equilibrium equations and satisfying the boundary conditions. In this new method there exists the flexibility to impose the physical conditions that govern the behavior of residual stress to achieve a meaningful complete stress field. The analysis is also coupled to a least squares approximation and a regularization method to provide stability of the inverse problem. The power of this new method is then demonstrated by analyzing some experimental measurements and achieving a good agreement between the model prediction and the results obtained from residual stress measurement.

Keywords: Residual stress, Limited measurements, Inverse problems, Turning process.

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Authors: Tariq T. Darabseh

Abstract:

The transient thermoelastic response of thick hollow cylinder made of functionally graded material under thermal loading is studied. The generalized coupled thermoelasticity based on the Green-Lindsay model is used. The thermal and mechanical properties of the functionally graded material are assumed to be varied in the radial direction according to a power law variation as a function of the volume fractions of the constituents. The thermal and elastic governing equations are solved by using Galerkin finite element method. All the finite element calculations were done by using commercial finite element program FlexPDE. The transient temperature, radial displacement, and thermal stresses distribution through the radial direction of the cylinder are plotted.

Keywords: Finite element method, thermal stresses, Green-Lindsay theory, functionally graded material.

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Authors: N. A. Salim, M. M. Othman, I. Musirin, M. S. Serwan

Abstract:

Hidden failure in a protection system has been recognized as one of the main reasons which may cause to a power system instability leading to a system cascading collapse. This paper presents a computationally systematic approach used to obtain the estimated average probability of a system cascading collapse by considering the effect of probability hidden failure in a protection system. The estimated average probability of a system cascading collapse is then used to determine the severe loading condition contributing to the higher risk of critical system cascading collapse. This information is essential to the system utility since it will assist the operator to determine the highest point of increased system loading condition prior to the event of critical system cascading collapse.

Keywords: Critical system cascading collapse, protection system hidden failure, severe loading condition.

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Authors: Mehrdad Mahmudizad, Roya Ahmadi Ahangar

Abstract:

This paper presents the method of designing the type 2 fuzzy PID controllers in order to solve the problem of Load Frequency Control (LFC). The Harmony Search (HS) algorithm is used to regulate the measurement factors and the effect of uncertainty of membership functions of Interval Type 2 Fuzzy Proportional Integral Differential (IT2FPID) controllers in order to reduce the frequency deviation resulted from the load oscillations. The simulation results implicitly show that the performance of the proposed IT2FPID LFC in terms of error, settling time and resistance against different load oscillations is more appropriate and preferred than PID and Type 1 Fuzzy Proportional Integral Differential (T1FPID) controllers.

Keywords: Load Frequency Control, Fuzzy-PID controller, Type 2 fuzzy system, Harmony Search algorithm.

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Authors: F. Vallée, J-F. Toubeau, Z. De Grève, J. Lobry

Abstract:

When evaluating the capacity of a generation park to cover the load in transmission systems, traditional Loss of Load Expectation (LOLE) and Expected Energy not Served (EENS) indices can be used. If those indices allow computing the annual duration and severity of load non covering situations, they do not take into account the fact that the load excess is generally shifted from one penury state (hour or quarter of an hour) to the following one. In this paper, a sequential Monte Carlo framework is introduced in order to compute adjusted LOLE and EENS indices. Practically, those adapted indices permit to consider the effect of load excess transfer on the global adequacy of a generation park, providing thus a more accurate evaluation of this quantity.

Keywords: Expected Energy not Served, Loss of Load Expectation, Monte Carlo simulation, reliability, wind generation.

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Authors: H. Shayeghi, H. Hosseini, A. Shabani, M. Mahdavi

Abstract:

In this paper, optimal generation expansion planning (GEP) is investigated considering purchase prices, profits of independent power producers (IPPs) and reliability criteria using a new method based on hybrid coded Genetic Algorithm (GA) and Particle Swarm Optimization (PSO). In this approach, optimal purchase price of each IPP is obtained by HCGA and reliability criteria are calculated by PSO technique. It should be noted that reliability criteria and the rate of carbon dioxide (CO2) emission have been considered as constraints of the GEP problem. Finally, the proposed method has been tested on the case study system. The results evaluation show that the proposed method can simply obtain optimal purchase prices of IPPs and is a fast method for calculation of reliability criteria in expansion planning. Also, considering the optimal purchase prices and profits of IPPs in generation expansion planning are caused that the expansion costs are decreased and the problem is solved more exactly.

Keywords: GEP Problem, IPPs, Reliability Criteria, GA, PSO.

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Authors: Saeed Mian Qaisar, Laurent Fesquet, Marc Renaudin

Abstract:

Mostly the real life signals are time varying in nature. For proper characterization of such signals, time-frequency representation is required. The STFT (short-time Fourier transform) is a classical tool used for this purpose. The limitation of the STFT is its fixed time-frequency resolution. Thus, an enhanced version of the STFT, which is based on the cross-level sampling, is devised. It can adapt the sampling frequency and the window function length by following the input signal local variations. Therefore, it provides an adaptive resolution time-frequency representation of the input. The computational complexity of the proposed STFT is deduced and compared to the classical one. The results show a significant gain of the computational efficiency and hence of the processing power. The processing error of the proposed technique is also discussed.

Keywords: Level Crossing Sampling, Activity Selection, Adaptive Resolution Analysis, Computational Complexity

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Authors: Abdelkrim Zitouni, Mounir Zid, Sami Badrouchi, Rached Tourki

Abstract:

The Globally Asynchronous Locally Synchronous Network on Chip (GALS NoC) is the most efficient solution that provides low latency transfers and power efficient System on Chip (SoC) interconnect. This study presents a GALS and generic NoC architecture based on a configurable router. This router integrates a sophisticated dynamic arbiter, the wormhole routing technique and can be configured in a manner that allows it to be used in many possible NoC topologies such as Mesh 2-D, Tree and Polygon architectures. This makes it possible to improve the quality of service (QoS) required by the proposed NoC. A comparative performances study of the proposed NoC architecture, Tore architecture and of the most used Mesh 2D architecture is performed. This study shows that Spidergon architecture is characterised by the lower latency and the later saturation. It is also shown that no matter what the number of used links is raised; the Links×Diameter product permitted by the Spidergon architecture remains always the lower. The only limitation of this architecture comes from it-s over cost in term of silicon area.

Keywords: Dynamic arbiter, Generic router, Spidergon NoC, SoC.

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Authors: Danielle Reichel, Antoine Druilhe, Tuan Dang

Abstract:

Traditional development of wireless sensor network mote is generally based on SoC1 platform. Such method of development faces three main drawbacks: lack of flexibility in terms of development due to low resource and rigid architecture of SoC; low capability of evolution and portability versus performance if specific micro-controller architecture features are used; and the rapid obsolescence of micro-controller comparing to the long lifetime of power plants or any industrial installations. To overcome these drawbacks, we have explored a new approach of development of wireless sensor network mote using a hybrid FPGA technology. The application of such approach is illustrated through the implementation of an innovative wireless sensor network protocol called OCARI.

Keywords: Hybrid FPGA, Embedded system, Mote, flexibility, durability, OCARI protocol, SoC, Wireless Sensor Network

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Authors: Elizabeth M. Hodge, Sharon K. Collins, Eric Kisling

Abstract:

Virtual environments are a hot topic in academia and more importantly in courses offered via distance education. Today-s gaming generation view virtual worlds as strong social and interactive mediums for communicating and socializing. And while institutions of higher education are challenged with increasing enrollment while balancing budget cuts, offering effective courses via distance education become a valid option. Educators can utilize virtual worlds to offer students an enhanced learning environment which has the power to alleviate feelings of isolation through the promotion of communication, interaction, collaboration, teamwork, feedback, engagement and constructivists learning activities. This paper focuses on the use of virtual environments to facilitate interaction in distance education courses so as to produce positive learning outcomes for students. Furthermore, the instructional strategies were reviewed and discussed for use in virtual worlds to enhance learning within a social context.

Keywords: Virtual Environments, Second Life, Instructional Strategies and Technology

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Authors: Kolay P. K., Singh H.

Abstract:

The coal utilization in thermal power plants in Malaysia has increased significantly which produces an enormous amount of coal combustion by-product (CCBP) or coal ash and poses severe disposal problem. As each coal ash is distinct, this study presents the geochemistry of the coal ash, in particular fly ash, produced from the combustion of local coal from Kuching Sarawak, Malaysia. The geochemical composition of the ash showed a high amount of silica, alumina, iron oxides and alkalies which was found to be a convenient starting material for the hydrothermal synthesis of zeolites with the higher Na₂O percentage being a positive factor for its alkaline activation; while the mineral phases are mainly quartz, mullite, calcium oxide, silica, and iron oxide hydrate. The geochemical changes upon alkali activation that can be predicted in a similar type of ash have been described in this paper. The result shows that this particular ash has a good potential for a high value industrial product like zeolites upon alkali activation.

Keywords: Coal ash, chemical composition, mineralogical composition, alkali activation, SEM.

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Authors: M. A. Abd-Allah, Mahmoud N. Ali, A. Said

Abstract:

Lightning protection systems (LPS) for wind power generation is becoming an important public issue. A serious damage of blades, accidents where low-voltage and control circuit breakdowns are frequently occur in many wind farms. A grounding system is one of the most important components required for appropriate LPSs in wind turbines WTs. Proper design of a wind turbine grounding system is demanding and several factors for the proper and effective implementation must taken into account. In this paper proposed procedure of proper design of grounding systems for a wind turbine was introduced. This procedure depends on measuring of ground current of simulated wind farm under lightning taking into consideration the soil ionization. The procedure also includes the Ground Potential Rise (GPR) and the voltage distributions at ground surface level and Touch potential. In particular, the contribution of mitigating techniques, such as rings, rods and the proposed design were investigated.

Keywords: WTs, LPS, GPR, Grounding System, Mitigating techniques.

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Authors: Victor Oluwaseyi Olowonisi

Abstract:

The paper aimed at presenting an overview on the concept of e-learning as it relates to higher education and how it provides opportunities for students, instructors and the government in developing the educational sector. It also touched on the benefits and challenges attached to e-learning as a new medium of reaching more students especially in the Nigerian context. The opportunities attributed to e-learning in the paper includes breaking boundaries barriers, reaching a larger number of students, provision of jobs for ICT experts, etc. In contrary, poor power supply, cost of implementation, poor computer literacy, technophobia (fear of technology), computer crime and system failure were some of the challenges of e-learning discussed in the paper. The paper proffered that the government can help the people gain more from e-learning through its financing. Also, it was stated that instructors/lecturers and students need to undergo training on computer application in order for e-learning to be more effective in developing higher education in Nigeria.

Keywords: E-Learning, education, higher education, increasing literacy.

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Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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